|
Size: 2601
Comment:
|
Size: 1826
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| * Brik2Bfloat brik2bfloat * MincToBshort minc_to_bshort * MkXsubjReg mkxsubjreg * MriAddXformToHeader mri_add_xform_to_header * MriAnnotation2Label mri_annotation2label * MriAverage mri_average * MriCaLabel mri_ca_label * MriCaNormalize mri_ca_normalize * MriCaRegister mri_ca_register * MriCaTrain mri_ca_train * MriConvert mri_convert * MriConvertMdh mri_convert_mdh * MriCor2Label mri_cor2label * MriEmRegister mri_em_register * MriFill mri_fill * MriGdfGlm mri_gdfglm * MriHead mri_head * MriInfo mri_info * MriLabel2Label mri_label2label * MriLabelVolume mri_label_volume * MriLinearRegister mri_linear_register * MriMakeRegister mri_make_register * MriMakeTemplate mri_make_template * MriMatrixMultiple mri_matrix_multiply * MriMsFitParms mri_ms_fitparms * MriNormalize mri_normalize * MriParseSdcmDir mri_parse_sdcmdir * MriPartialRibbon mri_partial_ribbon * MriProbdeDicom mri_probedicom * MriProbeIma mri_probe_ima * MriRegister mri_register * MriRelabelHypointensities mri_relabel_hypointensities * MriRigidRegister mri_rigid_register * MriSegHead mri_seghead * MriSegment mri_segment * MriStripSkull mri_strip_skull * MriSurf2Surf mri_surf2surf * MriSurf2Vol mri_surf2vol * MriSurfCluster mri_surfcluster * MriTessellate mri_tessellate * MriVol2Roi mri_vol2roi * MriVol2Surf mri_vol2surf * MriVolCluster mri_volcluster * MriVolSynth mri_volsynth * MriWmFilter mri_wmfilter * MriWatershed mri_watershed * MriXvolAvg mri_xvolavg * Mris2Rgb mris2rgb * MrisAnatomicalStats mris_anatomical_stats * MrisAverageCurvature mris_average_curvature * MrisCaLabel mris_ca_label * MrisCaTrain mris_ca_train * MrisConvert mris_convert * MrisCurvature mris_curvature * MrisEulerNumber mris_euler_number * MrisFindFlatRegions mris_find_flat_regions * MrisFixTopology mris_fix_topology * MrisFlatten mris_flatten * MrisGlm mris_glm * MrisInflate mris_inflate * MrisMakeAvergeSurface mris_make_average_surface * MrisMakeSurfaces mris_make_surfaces * MrisMakeTemplate mris_make_template * MrisRegister mris_register * MrisSmooth mris_smooth * MrisSphere mris_sphere * MrisSphericalAverage mris_spherical_average * MrisThickness mris_thickness * MrisTwoClass mris_twoclass * MrispPaint mrisp_paint * MriSynthesize mri_synthesize * NMovie nmovie * OptSeq2 optseq2 * Paint paint * Spm2Bfloat spm2bfloat * StatCombine statcombine * StatNormalize stat_normalize * VssDump vss-dump |
#pragma section-numbers on <<Include(Blank, "Recon-all", 4)>> * [[recon-all]] * Commands, in chronological order: * [[mri_convert]] * [[mri_robust_template]] * [[mri_nu_correct.mni]] * [[talairach]] * [[mri_normalize]] * [[mri_watershed]] * [[mri_em_register]] * [[mri_ca_normalize]] * [[mri_ca_register]] * [[mri_remove_neck]] * [[mri_ca_label]] * [[mri_segstats]] * [[mri_mask]] * [[mri_segment]] * [[mri_edit_wm_with_aseg]] * [[mri_pretess]] * [[mri_fill]] * [[mri_tessellate]] * [[mris_smooth]] * [[mris_inflate]] * [[mris_sphere]] * [[mris_fix_topology]] * [[mris_make_surfaces]] * [[mris_surf2vol]] * [[mris_register]] * [[mrisp_paint]] * [[mris_ca_label]] * [[mris_anatomical_stats]] * [[mri_aparc2aseg]] <<Include(Blank, "Volume", 4)>> <<Include(FreeSurferCommandsVolumeConversion, , 5)>> <<Include(FreeSurferCommandsMotionCorrection, , 5)>> <<Include(FreeSurferCommandsTalairach, ,5)>> <<Include(FreeSurferCommandsIntensityNormalization, ,5)>> <<Include(FreeSurferCommandsSkullStripping, ,5)>> <<Include(FreeSurferCommandsSegmentation, ,5)>> <<Include(FreeSurferCommandsVolumeMisc, ,5)>> <<Include(Blank, "Surface", 4)>> <<Include(FreeSurferCommandsSurfaceGeneration, ,5)>> <<Include(FreeSurferCommandsSurfaceSmoothing, ,5)>> <<Include(FreeSurferCommandsSurfaceInflation, ,5)>> <<Include(FreeSurferCommandsTopologyFixing, ,5)>> <<Include(FreeSurferCommandsInterSubjectMorphing, ,5)>> <<Include(FreeSurferCommandsFinalSurfaceGeneration, ,5)>> <<Include(FreeSurferCommandsSurfaceParcellation, ,5)>> <<Include(FreeSurferCommandsFlattening, ,5)>> <<Include(FreeSurferCommandsSurfaceMisc, ,5)>> <<Include(Blank, "Registration", 4)>> <<Include(FreeSurferCommandsRegistration, ,5)>> |
- Commands, in chronological order:
Freesurfer comes with a variety of different registration tools designed for specific purposes. This page is supposed to highlight a few of them and describe the context in which they should be used:
1. mri_robust_register
mri_robust_register: 2 inputs, rigid/affine, same or cross-modality, unbiased
A tool for pairwise image registration. Originally designed for highly accurate same modality and same subject registration (across time). It can compute rigid or affine transforms. It is robust with respect to outlier/anatomy change (removing their influence in the registration) and is inverse consistent (symmetric). More recent versions (dev) are capable of registering across modality in a symmetric fashion. robust_register is also used to register histology scans (part to whole hemisphere), etc.
2. mri_robust_template
mri_robust_template: n inputs, rigid/affine, same-modality, unbiased
A tool to register several inputs (same modality) to an unbiased average template, that it creates at the same time. Registration can be rigid or affine. Inputs are usually of the same subject, e.g. at different times. robust_template is based on robust_register and inherits the robustness to outlier. It is used in recon-all in the motion correction step (to co-register several within session scans to create one higher SNR input) and for longitudinal processing to create the unbiased average template.
3. bbregister
bbregister: 2 inputs, rigid, cross-modality, needs surfaces
This program performs within-subject, cross-modal registration using a boundary-based cost function. The registration is can be 6, 9, or 12 DOF DOF (rigid-to-affine). It is required that you have an anatomical scan of the subject that has been processed in Freesurfer.
4. mri_cvs_register
mri_cvs_register: 2 inputs, non-linear, same-modality, needs surfaces
This program performs subject-to-subject or subject-to-atlas non-linear volume registration using a combined volumetric and surface-based (CVS) registration algorithm. It is required that you have an anatomical scan of the subject that has been processed in Freesurfer!
5. mri_em_register
mri_em_register: 2 inputs, linear, atlas registration
This generates a linear talairach transform (lta file) from T1 anatomical to gca file (probabilistic atals). It is used in recon-all to create transforms/talairach.lta .
6. mri_ca_register
mri_ca_register: 2 inputs, non-linear, atlas registration
This generates a multi-dimensional talairach transform from T1 anatomical to a gca file (probabilistic atals) using a linear talairach (registration) file as initialization. It is used in recon-all to create transforms/talairach.m3z .
7. other registration tools
tkregister - graphical tool to manually register two images
FreeView - graphical viewer that can also do simple rotations, cropping
8. deprecated
orient_mri - graphically and interactively re-orient an MRI volume and save the new transform